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Help needed with Repetier and sli3er (no replies)

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There is probably a very simple solution to this and I am sorry if this is littered all over the internet but after taking a few googles and scrolls through the forums I couldn't find the answer..
When I launch Repetier and connect to the printer everything is fine. When I go to manual controls I can control each of the axises and they seem to move at the correct scale. I can then set the home to bottom left hand corner with the nozzle touching the table..So far so good.
I then load a calibration cube (stl file) which automatically centres and use sli3er to create the g-code,,
When i run the operation the scales seem to be way off. . The z-axis raises and starts to print at around 100mm off the table. The also doesn't print in the centre. it prints to the far right of the table, usually trying to force itself further than the tracks allow.
When i press "emergency stop" or "kill" it stops the printing and when i manually control the printer to go back to zero it no longer is at the bottom left hand corner, but closer to the centre.
Any help you can give me would be much appreciated. I hope you can understand my messy explanation.
Many thanks and hope to hear from someone soon.

PS: I started working with Repetier only just today and never used sli3er before.. I am using "Repetier-Host Windows 0.90C"

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